How can I seal/close a head model at the bottom so no light will get in but only from the eyes?
Firstly, you are not only selecting the vertices around the hole—only select the vertices that are actually "touching the hole" (if that makes sense). If it's still not working, it's likely you're having some sort of issue with the mirror modifier. Try applying the modifier, select all, and then W-->remove doubles. Select all of the vertices surrounding the hole, and then press "F." This should fill it up nicely.